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Ranaghan KE, Morris WG, Masgrau L, Senthilkumar K, Johannissen LO, Scrutton NS, Harvey JN, Manby FR, Mulholland AJ. Ab Initio QM/MM Modeling of the Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic Amine Dehydrogenase. J Phys Chem B 2017; 121:9785-9798. [PMID: 28930453 DOI: 10.1021/acs.jpcb.7b06892] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aromatic amine dehydrogenase (AADH) and related enzymes are at the heart of debates on the roles of quantum tunneling and protein dynamics in catalysis. The reaction of tryptamine in AADH involves significant quantum tunneling in the rate-limiting proton transfer step, shown by large H/D primary kinetic isotope effects (KIEs), with unusual temperature dependence. We apply correlated ab initio combined quantum mechanics/molecular mechanics (QM/MM) methods, at levels up to local coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), to calculate accurate potential energy surfaces for this reaction, which are necessary for quantitative analysis of tunneling contributions and reaction dynamics. Different levels of QM/MM treatment are tested. Multiple pathways are calculated with fully flexible transition state optimization by the climbing-image nudged elastic band method at the density functional QM/MM level. The average LCCSD(T) potential energy barriers to proton transfer are 16.7 and 14.0 kcal/mol for proton transfer to the two carboxylate atoms of the catalytic base, Asp128β. The results show that two similar, but distinct pathways are energetically accessible. These two pathways have different barriers, exothermicity and curvature, and should be considered in analyses of the temperature dependence of reaction and KIEs in AADH and other enzymes. These results provide a benchmark for this prototypical enzyme reaction and will be useful for developing empirical models, and analyzing experimental data, to distinguish between different conceptual models of enzyme catalysis.
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Affiliation(s)
- Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - William G Morris
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Laura Masgrau
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona , 08193 Bellaterra (Barcelona), Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona , 08193 Bellaterra (Barcelona), Spain
| | | | - Linus O Johannissen
- Manchester Institute of Biotechnology, University of Manchester , Manchester M13 9PL, U.K
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, University of Manchester , Manchester M13 9PL, U.K
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven , Celestijnenlaan 200F, B-3001 Heverlee, Belgium
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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McGeagh JD, Ranaghan KE, Mulholland AJ. Protein dynamics and enzyme catalysis: insights from simulations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1077-92. [PMID: 21167324 DOI: 10.1016/j.bbapap.2010.12.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 11/25/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to make of the ferocious arguments in this area? Protein dynamics are complex and fascinating, as molecular dynamics simulations and experiments have shown. The essential question is: do these complex motions have functional significance? In particular, how do they affect or relate to chemical reactions within enzymes, and how are chemical and conformational changes coupled together? Biomolecular simulations can analyse enzyme reactions and dynamics in atomic detail, beyond that achievable in experiments: accurate atomistic modelling has an essential part to play in clarifying these issues. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- John D McGeagh
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS, United Kingdom
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